Questions tagged [ucsc]

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4 votes
1 answer
92 views

Where can I find lncRNA expression data for different cell types?

Are there any publicly available databases providing expression data for long non-coding RNAs (lncRNAs) across cell types of multicellular organisms? Alternatively, are there lesser known UCSC tracks ...
2 votes
0 answers
21 views

How come bigWigSummary shows coverage greater than 1 for some region of the genome?

I am running this command, using the UCSC utilities: bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1 to get phastCons77way ...
7 votes
1 answer
2k views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
1 vote
0 answers
53 views

ucsc-bedgraphtobigwig throwing memory allocation error

I installed the latest ucsc-bedgraphtobigwig (v377) with conda in a new enviroment enviroment inmy WSL2. conda install -c bioconda ucsc-bedgraphtobigwig However, ...
6 votes
2 answers
51 views

How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?

I want to display E.coli BW25113 (GenBank: CP009273.1) strain in UCSC browser. This strain is not listed in http://microbes.ucsc.edu/ browser. How can I display E.coli BW25113 assembly in the browser?
3 votes
0 answers
50 views

Command line based interaction with the UCSC genome browser, automated data upload and track generation

Is there a way to submit data to ucsc genome browser for result/track display, on the fly, as a local bedgraph file with example contents like below: ...
1 vote
0 answers
17 views

Running hubCheck utility from inside K8s's Pod

I'm trying to run hubCheck utility* from inside Kubernetes Pod but for some reason I get this Network error: ...
2 votes
1 answer
75 views

Hg38 annotation tracks retrieval

I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes"...
-1 votes
1 answer
301 views

What's the meaning of Txn factor?

The transcription factor track in UCSC is named as Txn factor. Why Txn == Transcription?
0 votes
1 answer
90 views

How can I add for several bed files the header : track type=narrowPeak name=“narrowPeak” preferably in python ,can handle with R

I want to create custom tracks from these files I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor: track type=narrowPeak name=“narrowPeak” but I ...
0 votes
1 answer
420 views

How to visualize called narrowPeak files in UCSC Genome browser? [closed]

I have this file: and I get this error I googled and found this solution but it still doesn't work and I get this error Error File 'GSM2797523_FOXA2_IDR0.02_narrowPeak_try.bed' - line 1 of custom ...
1 vote
1 answer
2k views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
0 votes
1 answer
103 views

How to annotate gene length to a list of gene symbols using UCSC data?

I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
2 votes
1 answer
65 views

Efficiently concatenating disjoint, ordered bigBed files

Given a set of bigBed files, each of which are disjoint to each other and in lexicographical ("sort-bed") sort order, I would like to know if there is a way to concatenate these archives efficiently. ...
2 votes
1 answer
103 views

UCSC liftover cannot produce bed format output

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didn't: ...
0 votes
1 answer
171 views

What is the `table` parameter in the UCSU ldHgGene tool?

I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. I got the chain file for the final step and ran: ...
0 votes
1 answer
213 views

UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux

I have installed some ucsc tools on my Mac computer and it worked fine: Installation ...
1 vote
1 answer
152 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
3 votes
1 answer
114 views

Finding URL for UCSC data hub

I am trying to build a UCSC track hub (a private one). I have all my hub files on a university server in a simple folder called /hub. I am using Ubuntu 16.04 and the server is also Ubuntu (16.04.3 ...
1 vote
0 answers
140 views

Question: UCSC hub: autoscale option for multiwig track

I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale:...
0 votes
1 answer
205 views

Does the galGal5 chicken assembly have a chromosome 29?

The chromosome sizes at UCSC don't seem to contain chr29: ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.chrom.sizes It has a chr28 and a chr30. Am I missing something or is there ...
0 votes
1 answer
106 views

differentially expressed intron analysis?

I have used Deseq for estimating the differentially expressed introns for the RNA seq data using the UCSC intron bed file. can Deseq be used for differentially expressed intron analysis?
5 votes
1 answer
76 views

How are positions visually indicated in the UCSC Genome Browser?

I'm a little confused about how the position indices work in the browser. Based on the picture below, is base number 755440 an A or a ...
2 votes
1 answer
35 views

Link to UCSC gtexGene track description page for selected gene symbol

I have this link that comes up when I am in the browser window and click on the gene name, which leads me to description page about the gene (in this example it is BOK gene). How can I generate that ...
1 vote
2 answers
88 views

Get gene exons from UCSC browser by HGNC name

I have a set of gene names in HGNC standard and I want to get all their exons (in BED format) from the UCSC browser but it seems like the browser doesn't index genes by their HGNC name. How can I do ...
1 vote
1 answer
34 views

Hba-a2 has two copies on UCSC genome browser

I was browsering the UCSC viewer of the genome at this region. UCSC genes label two genes as Hba-a2 while GENCODE thinks the left one is Hba-a1 Which annotation is correct?
1 vote
1 answer
498 views

How can I download genePred file from UCSC?

I need a gtf annotation file. UCSC doesn't give us a proper gtf file with distinct gene_id and transcript_id. It asked us to get a genePred file to convert to gtf. But where can we get genePred files?...
4 votes
1 answer
492 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...